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- PDB-7jgu: Structure of FN3tt mut -

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Basic information

Entry
Database: PDB / ID: 7jgu
TitleStructure of FN3tt mut
ComponentsFibronectin type-III domain-containing protein
KeywordsSTRUCTURAL PROTEIN / FN3-like domain / Hyperthermal stability / Surface Salt Bridges
Function / homology
Function and homology information


: / IPT/TIG domain / ig-like, plexins, transcription factors / IPT domain / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Fibronectin type-III domain-containing protein
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLuo, J. / Boucher, L.E.
CitationJournal: Proteins / Year: 2022
Title: Surface salt bridges contribute to the extreme thermal stability of an FN3-like domain from a thermophilic bacterium.
Authors: Boucher, L. / Somani, S. / Negron, C. / Ma, W. / Jacobs, S. / Chan, W. / Malia, T. / Obmolova, G. / Teplyakov, A. / Gilliland, G.L. / Luo, J.
History
DepositionJul 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibronectin type-III domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4142
Polymers11,1751
Non-polymers2381
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.000, 38.310, 28.180
Angle α, β, γ (deg.)90.000, 103.880, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-227-

HOH

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Components

#1: Protein Fibronectin type-III domain-containing protein


Mass: 11175.329 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) (bacteria)
Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: TTE0165 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RD81
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5 / Details: 25% PEG 3350, 0.2M sodium di-hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→27.36 Å / Num. obs: 34160 / % possible obs: 99 % / Redundancy: 3.184 % / Biso Wilson estimate: 19.682 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.06 / Χ2: 0.93 / Net I/σ(I): 12.39 / Num. measured all: 108762 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.2-1.232.9210.9232.557379254325260.5431.12899.3
1.23-1.263.0440.7283.017404246624320.6840.88298.6
1.26-1.33.0890.5263.887328239323720.7780.63999.1
1.3-1.343.2110.4164.677521236023420.8580.50299.2
1.34-1.393.2420.3355.877206223922230.8710.40399.3
1.39-1.433.2270.28177090220321970.8970.33899.7
1.43-1.493.1640.2258.026715213421220.9370.27199.4
1.49-1.553.1930.15910.16396200520030.9670.19199.9
1.55-1.623.4310.1212.326649194619380.9790.14299.6
1.62-1.73.4230.09414.416456189418860.9860.11299.6
1.7-1.793.3190.07116.765832176617570.9920.08599.5
1.79-1.93.1960.0619.055426172516980.9930.07198.4
1.9-2.033.0550.0520.874683156515330.9940.06198
2.03-2.193.0520.04522.494453148514590.9960.05498.2
2.19-2.43.3430.04224.684466135113360.9960.0598.9
2.4-2.683.3010.03925.484054124712280.9960.04798.5
2.68-3.13.1660.03725.753394108310720.9970.04499
3.1-3.792.990.03525.9227519549200.9960.04396.4
3.79-5.373.1780.03727.1822637237120.9960.04498.5
5.37-27.363.2080.03527.1812964194040.9960.04296.4

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JGT

7jgt


Resolution: 1.2→27.36 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1809 1707 5 %
Rwork0.149 32451 -
obs0.1505 34158 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.71 Å2 / Biso mean: 24.7027 Å2 / Biso min: 8.07 Å2
Refinement stepCycle: final / Resolution: 1.2→27.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms706 0 38 97 841
Biso mean--66.17 36.18 -
Num. residues----90
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.240.32641420.2962697283999
1.24-1.280.3041400.28572673281399
1.28-1.320.30931420.25982695283799
1.32-1.370.25451410.19842680282199
1.37-1.440.1981420.146926982840100
1.44-1.510.15741420.129626982840100
1.51-1.610.1541440.124527322876100
1.61-1.730.14581420.11926972839100
1.73-1.90.14261430.12062726286999
1.9-2.180.14741420.12462684282698
2.18-2.750.17151420.15022710285299
2.75-27.360.19011450.14952761290698

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